segfault after installing only R in a fresh environment

[jnrunge]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Issue: new versions of R cannot be run, even in a fresh environment. They install just fine (mamba create -p xyz -c conda-forge r-base=4.2), but once I try to run them (R), they crash immediately upon start with the following error:

*** caught segfault ***
address (nil), cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Segmentation fault (core dumped)

gdb reveals additional details:

 Program terminated with signal 11, Segmentation fault.
#0  0x00002aaaab4ecf81 in __strlen_sse2_pminub () from /lib64/libc.so.6

(The conda info and conda list data is from the 4.2 environment)

The last R version that still works fine with a simple mamba install/create ist 3.4.1. I used to be able to install R 3.6.1 years ago on this system, which still works, but cannot be replicated now, so I investigated where the error started.

Within 3.5.1, which does not work after mamba install r-base=3.5.1, the last working version is hea2b9be_1007. From the next (h08e1455_1008) onwards, the error as described above results. It is a unclear to me how best to understand what changed between these two, but hopefully it helps you guys?

I am experiencing this issue on two, completely separate and indepdentely managed (not by me) linux x64 clusters (only similarity is my user account, but they were not copied over or anything), which is strange to me as all of you appear to be fine?!

I tried

• anaconda-clean
• switching to a fresh mambaforge install

Furthermore, maybe it helps to know that I cannot update/downgrade from 3.5.1 hea2b9be_1007 to h08e1455_1008 or vice versa (both can be installed in a fresh environment).

Update log (hea2b9be_1007 to h08e1455_1008) on cluster 1

Preparing transaction: failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1080, in __call__
        return func(*args, **kwargs)
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 882, in exception_converter
        raise e
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 876, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 835, in _wrapped_main
        result = do_call(args, p)
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 716, in do_call
        exit_code = install(args, parser, "install")
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 595, in install
        handle_txn(conda_transaction, prefix, args, newenv)
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 148, in handle_txn
        unlink_link_transaction.execute()
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 245, in execute
        self.verify()
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 222, in verify
        self.prepare()
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 211, in prepare
        grps = self._prepare(self.transaction_context, stp.target_prefix,
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 296, in _prepare
        python_version = cls._get_python_version(target_prefix,
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 821, in _get_python_version
        linked_python_version = get_python_version_for_prefix(target_prefix)
      File "/home/jnrunge/anaconda3/lib/python3.8/site-packages/conda/core/prefix_data.py", line 385, in get_python_version_for_prefix
        elif record.version[3].isdigit():
    IndexError: string index out of range

`$ /home/jnrunge/anaconda3/condabin/mamba install -c conda-forge r-base=3.5.1=h08e1455_1008`

  environment variables:
                 CIO_TEST=<not set>
        CMAKE_PREFIX_PATH=/home/jnrunge/r-3-5-1-cf:/home/jnrunge/r-3-5-1-cf/x86_64-conda-linux-
                          gnu/sysroot/usr
      CONDA_BUILD_SYSROOT=/home/jnrunge/r-3-5-1-cf/x86_64-conda-linux-gnu/sysroot
        CONDA_DEFAULT_ENV=/home/jnrunge/r-3-5-1-cf
                CONDA_EXE=/home/jnrunge/anaconda3/bin/conda
             CONDA_PREFIX=/home/jnrunge/r-3-5-1-cf
           CONDA_PREFIX_1=/home/jnrunge/anaconda3
    CONDA_PROMPT_MODIFIER=(/home/jnrunge/r-3-5-1-cf)
         CONDA_PYTHON_EXE=/home/jnrunge/anaconda3/bin/python
               CONDA_ROOT=/home/jnrunge/anaconda3
              CONDA_SHLVL=2
    CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
     CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
           CURL_CA_BUNDLE=<not set>
                 INFOPATH=/opt/rh/devtoolset-9/root/usr/share/info
                  MANPATH=/biotools/lmod/lmod/share/man:/opt/rh/devtoolset-9/root/usr/share/man:
               MODULEPATH=:/biotools/modules/bioinfo:/biotools/modules/core:/biotools/modules/bi
                          oinfo:/biotools/modules/core
                     PATH=/biotools/lmod/lmod/libexec:/home/jnrunge/r-3-5-1-cf/bin:/home/jnrunge
                          /anaconda3/condabin:/home/jnrunge/perl5/bin:/biotools/lmod/lmod/libexe
                          c:/opt/rh/devtoolset-9/root/usr/bin:/usr/local/bin:/usr/bin:/usr/local
                          /sbin:/usr/sbin:/home/jnrunge/.local/bin:/home/jnrunge/bin
          PKG_CONFIG_PATH=/opt/rh/devtoolset-9/root/usr/lib64/pkgconfig
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : /home/jnrunge/r-3-5-1-cf
    active env location : /home/jnrunge/r-3-5-1-cf
            shell level : 2
       user config file : /home/jnrunge/.condarc
 populated config files : /home/jnrunge/.condarc
          conda version : 4.11.0
    conda-build version : 3.21.4
         python version : 3.8.8.final.0
       virtual packages : __linux=3.10.0=0
                          __glibc=2.17=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/jnrunge/anaconda3  (writable)
      conda av data dir : /home/jnrunge/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/jnrunge/anaconda3/pkgs
                          /home/jnrunge/.conda/pkgs
       envs directories : /home/jnrunge/anaconda3/envs
                          /home/jnrunge/.conda/envs
               platform : linux-64
             user-agent : conda/4.11.0 requests/2.25.1 CPython/3.8.8 Linux/3.10.0-1160.53.1.el7.x86_64 centos/7.9.2009 glibc/2.17
                UID:GID : 1060:502
             netrc file : None
           offline mode : False

and on cluster 2:

Preparing transaction: failed
string index out of range

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
        return func(*args, **kwargs)
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/mamba/mamba.py", line 941, in exception_converter
        raise e
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/mamba/mamba.py", line 892, in _wrapped_main
        result = do_call(parsed_args, p)
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/mamba/mamba.py", line 754, in do_call
        exit_code = install(args, parser, "install")
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/mamba/mamba.py", line 599, in install
        handle_txn(conda_transaction, prefix, args, newenv)
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/mamba/linking.py", line 44, in handle_txn
        unlink_link_transaction.execute()
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/core/link.py", line 282, in execute
        self.verify()
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/common/io.py", line 84, in decorated
        return f(*args, **kwds)
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/core/link.py", line 232, in verify
        self.prepare()
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/core/link.py", line 221, in prepare
        grps = self._prepare(self.transaction_context, stp.target_prefix,
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/core/link.py", line 336, in _prepare
        python_version = cls._get_python_version(target_prefix,
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/core/link.py", line 873, in _get_python_version
        linked_python_version = get_python_version_for_prefix(target_prefix)
      File "/moto/ziab/users/jr3950/software/mambaforge/install/lib/python3.10/site-packages/conda/core/prefix_data.py", line 381, in get_python_version_for_prefix
        elif record.version[3].isdigit():
    IndexError: string index out of range

`$ /moto/ziab/users/jr3950/software/mambaforge/install/bin/mamba install -c conda-forge r-base=3.5.1=h08e1455_1008`

  environment variables:
                 CIO_TEST=<not set>
        CMAKE_PREFIX_PATH=/moto/ziab/users/jr3950/.conda/envs/r-3-5-1-
                          cf:/moto/ziab/users/jr3950/.conda/envs/r-3-5-1-cf/x86_64-conda-linux-
                          gnu/sysroot/usr
   CONDA_BACKUP_ADDR2LINE=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-addr2line
          CONDA_BACKUP_AR=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-ar
          CONDA_BACKUP_AS=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-as
       CONDA_BACKUP_BUILD=x86_64-conda-linux-gnu
          CONDA_BACKUP_CC=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-cc
CONDA_BACKUP_CC_FOR_BUILD=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-cc
      CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_CMAKE_PREFIX_PATH=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6:/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/x86_64-conda-linux-gnu/sysroot/usr
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/x86_64-conda-linux-gnu/sysroot
CONDA_BACKUP_CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
CONDA_BACKUP_CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
         CONDA_BACKUP_CPP=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-cpp
    CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
         CONDA_BACKUP_CXX=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-c++
     CONDA_BACKUP_CXXFILT=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-c++filt
    CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
                          -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_CXX_FOR_BUILD=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-c++
CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
                          -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
                          -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
                          -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
     CONDA_BACKUP_ELFEDIT=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-elfedit
         CONDA_BACKUP_F77=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gfortran
         CONDA_BACKUP_F90=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gfortran
         CONDA_BACKUP_F95=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-f95
          CONDA_BACKUP_FC=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gfortran
      CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/include
         CONDA_BACKUP_GCC=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gcc
      CONDA_BACKUP_GCC_AR=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gcc-ar
      CONDA_BACKUP_GCC_NM=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gcc-nm
  CONDA_BACKUP_GCC_RANLIB=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gcc-ranlib
    CONDA_BACKUP_GFORTRAN=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gfortran
       CONDA_BACKUP_GPROF=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-gprof
         CONDA_BACKUP_GXX=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-g++
        CONDA_BACKUP_HOST=x86_64-conda-linux-gnu
          CONDA_BACKUP_LD=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-ld
     CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,
                          --disable-new-dtags -Wl,--gc-sections
                          -Wl,-rpath,/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/lib -Wl,-rpath-
                          link,/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/lib -L/moto/ziab/users/jr3950/.conda/envs/my_conda-
                          defaults-channel-3.6/lib
     CONDA_BACKUP_LD_GOLD=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-ld.gold
  CONDA_BACKUP_MESON_ARGS=--buildtype release
          CONDA_BACKUP_NM=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-nm
     CONDA_BACKUP_OBJCOPY=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-objcopy
     CONDA_BACKUP_OBJDUMP=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-objdump
      CONDA_BACKUP_RANLIB=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-ranlib
     CONDA_BACKUP_READELF=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-readelf
        CONDA_BACKUP_SIZE=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-size
     CONDA_BACKUP_STRINGS=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-strings
       CONDA_BACKUP_STRIP=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-
                          channel-3.6/bin/x86_64-conda-linux-gnu-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
 CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu
  CONDA_BACKUP_host_alias=x86_64-conda-linux-gnu
      CONDA_BUILD_SYSROOT=/moto/ziab/users/jr3950/.conda/envs/r-3-5-1-cf/x86_64-conda-linux-
                          gnu/sysroot
        CONDA_DEFAULT_ENV=r-3-5-1-cf
                CONDA_EXE=/moto/ziab/users/jr3950/software/mambaforge/install/bin/conda
             CONDA_PREFIX=/moto/ziab/users/jr3950/.conda/envs/r-3-5-1-cf
           CONDA_PREFIX_1=/moto/ziab/users/jr3950/software/mambaforge/install
          CONDA_PREFIX_10=/moto/ziab/users/jr3950/.conda/envs/r-3-4-1-cf
           CONDA_PREFIX_2=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-channel
           CONDA_PREFIX_3=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-channel-3.6
           CONDA_PREFIX_4=/moto/ziab/users/jr3950/.conda/envs/my_conda2
           CONDA_PREFIX_5=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-channel-3.6
           CONDA_PREFIX_6=/moto/ziab/users/jr3950/.conda/envs/my_conda3
           CONDA_PREFIX_7=/moto/ziab/users/jr3950/.conda/envs/my_conda-defaults-channel-3.6
           CONDA_PREFIX_8=/moto/ziab/users/jr3950/.conda/envs/r-3-4-1-cf
           CONDA_PREFIX_9=/moto/ziab/users/jr3950/.conda/envs/r-3-5-1-cf
    CONDA_PROMPT_MODIFIER=(r-3-5-1-cf)
         CONDA_PYTHON_EXE=/moto/ziab/users/jr3950/software/mambaforge/install/bin/python
               CONDA_ROOT=/moto/ziab/users/jr3950/software/mambaforge/install
              CONDA_SHLVL=11
    CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
     CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
                    CPATH=/cm/shared/apps/slurm/20.11.9/include
           CURL_CA_BUNDLE=<not set>
          LD_LIBRARY_PATH=/cm/shared/apps/slurm/20.11.9/lib64/slurm:/cm/shared/apps/slurm/20.11.
                          9/lib64
               LD_PRELOAD=<not set>
             LIBRARY_PATH=/cm/shared/apps/slurm/20.11.9/lib64/slurm:/cm/shared/apps/slurm/20.11.
                          9/lib64
                  MANPATH=/cm/shared/apps/slurm/20.11.9/man:/usr/share/lmod/lmod/share/man:/usr/
                          local/share/man:/usr/share/man/overrides:/usr/share/man:/cm/local/apps
                          /environment-modules/current/share/man
               MODULEPATH=/cm/local/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/usr/sha
                          re/Modules/modulefiles:/cm/shared/modulefiles
                     PATH=/moto/ziab/users/jr3950/.conda/envs/r-3-5-1-
                          cf/bin:/moto/ziab/users/jr3950/.conda/envs/my_conda2/bin:/cm/shared/ap
                          ps/slurm/20.11.9/sbin:/cm/shared/apps/slurm/20.11.9/bin:/moto/ziab/use
                          rs/jr3950/software/anaconda/installed/condabin:/usr/local/bin:/usr/bin
                          :/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/moto/home/jr3950/bi
                          n
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
   __LMOD_REF_COUNT_CPATH=/cm/shared/apps/slurm/20.11.9/include:1
__LMOD_REF_COUNT_LD_LIBRARY_PATH=/cm/shared/apps/slurm/20.11.9/lib64/slurm:1;/cm/shared/apps/slurm/20.1
                          1.9/lib64:1
__LMOD_REF_COUNT_LIBRARY_PATH=/cm/shared/apps/slurm/20.11.9/lib64/slurm:1;/cm/shared/apps/slurm/20.1
                          1.9/lib64:1
 __LMOD_REF_COUNT_MANPATH=/cm/shared/apps/slurm/20.11.9/man:1;/usr/share/lmod/lmod/share/man:1;/
                          usr/local/share/man:1;/usr/share/man/overrides:1;/usr/share/man:1;/cm/
                          local/apps/environment-modules/current/share/man:3
    __LMOD_REF_COUNT_PATH=/cm/shared/apps/slurm/20.11.9/sbin:1;/cm/shared/apps/slurm/20.11.9/bin
                          :1;/moto/ziab/users/jr3950/software/anaconda/installed/condabin:1;/usr
                          /local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/opt/dell/srvadm
                          in/bin:1;/moto/home/jr3950/bin:1

     active environment : /moto/ziab/users/jr3950/.conda/envs/r-3-5-1-cf
    active env location : /moto/ziab/users/jr3950/.conda/envs/r-3-5-1-cf
            shell level : 11
       user config file : /moto/home/jr3950/.condarc
 populated config files : /moto/ziab/users/jr3950/software/mambaforge/install/.condarc
                          /moto/home/jr3950/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /moto/ziab/users/jr3950/software/mambaforge/install  (writable)
      conda av data dir : /moto/ziab/users/jr3950/software/mambaforge/install/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /moto/ziab/users/jr3950/software/mambaforge/install/pkgs
                          /moto/home/jr3950/.conda/pkgs
       envs directories : /moto/ziab/users/jr3950/software/mambaforge/install/envs
                          /moto/home/jr3950/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Linux/3.10.0-862.el7.x86_64 rhel/7.5 glibc/2.17
                UID:GID : 514969:500
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

Any help is greatly appreciated! Thanks. :smile

Installed packages

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0            h35add3b_1015    conda-forge
curl                      7.88.1               hdc1c0ab_1    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    12.2.0              h55be85b_19    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gxx_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
harfbuzz                  6.0.0                h3ff4399_1    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   7.88.1               hdc1c0ab_1    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     12.2.0              h3b97bd3_19    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.74.1               h606061b_1    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsanitizer              12.2.0              h46fd767_19    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-devel_linux-64  12.2.0              h3b97bd3_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.5.0                ha587672_6    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.3               hfdac1af_6    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
openssl                   3.1.0                h0b41bf4_0    conda-forge
pango                     1.50.14              hd33c08f_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
r-base                    4.2.3                h4a03800_2    conda-forge
readline                  8.2                  h8228510_1    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.8.4                h0b41bf4_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Environment info

active environment : /moto/ziab/users/jr3950/.conda/envs/my_conda3-re
    active env location : /moto/ziab/users/jr3950/.conda/envs/my_conda3-re
            shell level : 13
       user config file : /moto/home/jr3950/.condarc
 populated config files : /moto/ziab/users/jr3950/software/mambaforge/install/.condarc
                          /moto/home/jr3950/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /moto/ziab/users/jr3950/software/mambaforge/install  (writable)
      conda av data dir : /moto/ziab/users/jr3950/software/mambaforge/install/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /moto/ziab/users/jr3950/software/mambaforge/install/pkgs
                          /moto/home/jr3950/.conda/pkgs
       envs directories : /moto/ziab/users/jr3950/software/mambaforge/install/envs
                          /moto/home/jr3950/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Linux/3.10.0-862.el7.x86_64 rhel/7.5 glibc/2.17
                UID:GID : 514969:500
             netrc file : None
           offline mode : False

[mfansler]

I'd guess it's the LD_LIBRARY_PATH coming from your system. Can you check what ldd outputs on the R binary and the libR.so? They would be in somewhere like ${CONDA_PREFIX}/lib/R/bin/exec/R and ${CONDA_PREFIX}/lib/R/lib/libR.so.

Also see if you still get an error after clearing the LD_LIBRARY_PATH variable and running R.

[jnrunge]

EDIT
In case it matters:

uname -a
Linux bake 3.10.0-862.el7.x86_64 #1 SMP Wed Mar 21 18:14:51 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux


cat /etc/*release
Cluster Manager v8.1
slave
NAME="Red Hat Enterprise Linux Server"
VERSION="7.5 (Maipo)"
ID="rhel"
ID_LIKE="fedora"
VARIANT="Server"
VARIANT_ID="server"
VERSION_ID="7.5"
PRETTY_NAME="Red Hat Enterprise Linux"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:7.5:GA:server"
HOME_URL="https://www.redhat.com/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"

REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.5
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.5"
Red Hat Enterprise Linux Server release 7.5 (Maipo)
Red Hat Enterprise Linux Server release 7.5 (Maipo)

end EDIT

Thanks for your response.

There was a $LD_LIBRARY_PATH set (/cm/shared/apps/slurm/20.11.9/lib64/slurm:/cm/shared/apps/slurm/20.11.9/lib64), but even after unsetting it (echoing it gives an empty line), the error remains.

The ldd commands show the library in question of the gdb (libc.so.6), among others, to be linked outside of the conda environment (output at the end). These libraries are not present in R's library directory. Some of those libraries, including the
offending one, are present in ${CONDA_PREFIX}/x86_64-conda-linux-gnu/sysroot/lib64/, but those appear not to be used according to the ldd? However, I tried forcing this folder to be used, but this did not work either. Is there something there that could be the issue?

below is the output for trying to use this folder as library path. at the end is the original output

export LD_LIBRARY_PATH=/moto/ziab/users/jr3950/.conda/envs/my_conda3/x86_64-conda-linux-gnu/sysroot/lib64/
ldd /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/R
/usr/bin/bash: /moto/ziab/users/jr3950/.conda/envs/my_conda3/x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/bin/bash)
/usr/bin/bash: /moto/ziab/users/jr3950/.conda/envs/my_conda3/x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6: version `GLIBC_2.15' not found (required by /usr/bin/bash)
/usr/bin/bash: /moto/ziab/users/jr3950/.conda/envs/my_conda3/x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6: version `GLIBC_2.14' not found (required by /lib64/libtinfo.so.5)
/usr/bin/bash: /moto/ziab/users/jr3950/.conda/envs/my_conda3/x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6: version `GLIBC_2.15' not found (required by /lib64/libtinfo.so.5)

Thanks a lot!

ldd /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/R
 linux-vdso.so.1 =>  (0x00002aaaaaacd000)
 libR.so => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/libR.so (0x00002aaaaaccf000)
 libc.so.6 => /lib64/libc.so.6 (0x00002aaaab1a3000)
 libblas.so.3 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libblas.so.3 (0x00002aaaab570000)
 libm.so.6 => /lib64/libm.so.6 (0x00002aaaad818000)
 libreadline.so.8 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libreadline.so.8 (0x00002aaaaaaf5000)
 libpcre2-8.so.0 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libpcre2-8.so.0 (0x00002aaaaab4e000)
 liblzma.so.5 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../liblzma.so.5 (0x00002aaaaabef000)
 libbz2.so.1.0 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libbz2.so.1.0 (0x00002aaaaac18000)
 libz.so.1 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libz.so.1 (0x00002aaaaac2c000)
 librt.so.1 => /lib64/librt.so.1 (0x00002aaaadb1a000)
 libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaadd22000)
 libiconv.so.2 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libiconv.so.2 (0x00002aaaadf26000)
 libicuuc.so.72 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libicuuc.so.72 (0x00002aaaae00d000)
 libicui18n.so.72 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libicui18n.so.72 (0x00002aaaae214000)
 libgomp.so.1 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../libgomp.so.1 (0x00002aaaae544000)
 libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaae63e000)
 /lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)
 libgfortran.so.5 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../.././libgfortran.so.5 (0x00002aaaae85a000)
 libtinfo.so.6 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../.././libtinfo.so.6 (0x00002aaaaac4a000)
 libicudata.so.72 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../.././libicudata.so.72 (0x00002aaaaea05000)
 libstdc++.so.6 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../.././libstdc++.so.6 (0x00002aaab07d6000)
 libgcc_s.so.1 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../.././libgcc_s.so.1 (0x00002aaaaac8b000)
 libquadmath.so.0 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/bin/exec/../../lib/../../././libquadmath.so.0 (0x00002aaab098a000)

ldd /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/libR.so
 linux-vdso.so.1 =>  (0x00002aaaaaacd000)
 libblas.so.3 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libblas.so.3 (0x00002aaaab1a3000)
 libm.so.6 => /lib64/libm.so.6 (0x00002aaaad44b000)
 libreadline.so.8 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libreadline.so.8 (0x00002aaaaaaef000)
 libpcre2-8.so.0 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libpcre2-8.so.0 (0x00002aaaaab48000)
 liblzma.so.5 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../liblzma.so.5 (0x00002aaaaabe9000)
 libbz2.so.1.0 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libbz2.so.1.0 (0x00002aaaaac12000)
 libz.so.1 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libz.so.1 (0x00002aaaaac26000)
 librt.so.1 => /lib64/librt.so.1 (0x00002aaaad74d000)
 libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaad955000)
 libiconv.so.2 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libiconv.so.2 (0x00002aaaadb59000)
 libicuuc.so.72 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libicuuc.so.72 (0x00002aaaadc40000)
 libicui18n.so.72 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libicui18n.so.72 (0x00002aaaade47000)
 libgomp.so.1 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../libgomp.so.1 (0x00002aaaae177000)
 libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaae271000)
 libc.so.6 => /lib64/libc.so.6 (0x00002aaaae48d000)
 /lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)
 libgfortran.so.5 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../.././libgfortran.so.5 (0x00002aaaae85a000)
 libtinfo.so.6 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../.././libtinfo.so.6 (0x00002aaaaac44000)
 libicudata.so.72 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../.././libicudata.so.72 (0x00002aaaaea05000)
 libstdc++.so.6 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../.././libstdc++.so.6 (0x00002aaab07d6000)
 libgcc_s.so.1 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../.././libgcc_s.so.1 (0x00002aaaaac85000)
 libquadmath.so.0 => /moto/ziab/users/jr3950/.conda/envs/my_conda3/lib/R/lib/../../././libquadmath.so.0 (0x00002aaab098a000)

[mfansler]

Maybe try clearing the LD_LIBRARY_PATH before activating, then activate.

Might also be pertinent to know the terminal in use (e.g., tmux, vscode do weird things with env vars sometimes). And what is the environment activation command? (conda activate my_conda3?)

[jnrunge]

Tried this order and still the same:

unset LD_LIBRARY_PATH
mamba activate /moto/ziab/users/jr3950/.conda/envs/my_conda3

(using conda instead does not change things)

I am connecting via iTerm2 on macOS. Tried the built-in Mac terminal instead, no luck. I am usually using screen on the cluster, but not doing that did not help either. iTerm2 has a special script it adds on the server. I disabled that, re-connected, also no change.

A similar thing seems to be going on at StackOverflow just now, but I can't comment there.

[jnrunge]

The segfault disappears when running R without readline support: R --no-readline. I can also see that one of the changes from R 3.5.1 hea2b9be_1007 (working) to 3.5.1 h08e1455_1008 (not working) was going from readline 7.0 to readline 8.0. Is that helpful?

[mbargull]

Hi @jnrunge, thanks for the report!
I know it has been a while, but do you still have access to those systems?
If yes, could you try whether you can reproduce this when you set another locale via environment variables?
With the latest 4.4 builds, I can produce the following:

$ conda list '^(r-base|readline)$'
# packages in environment at /opt/conda/envs/r-base=4.4.1:
#
# Name                    Version                   Build  Channel
r-base                    4.4.1                h0be853a_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
$ locale -a
C
en_US.utf8
POSIX
$ LANG=C script /dev/null -qc 'R -q' < /dev/null
$ > 
$ LANG=en_US.UTF-8 script /dev/null -qc 'R -q' < /dev/null
$ > 
$ LANG=de_DE.UTF-8 script /dev/null -qc 'R -q' < /dev/null
$ During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

That one is pretty easy to solve for us since upstream already has a patch in, that we can just apply to our readline:
https://git.savannah.gnu.org/cgit/readline.git/commit/?id=7274faabe97ce53d6b464272d7e6ab6c1392837b